System Genesis
by Shinvitya
Summary: Three former children on the Von Braun. Crossover with System Shock 2.


Disclaimer: I don't own everything, NGE belongs to Anno and Gainax, System Shock belongs to Electronic Arts, which should belong to Irrational Games and/or Warren Spector.

**System Genesis**

* * *

Fire

Fire and Smoke was all that he could see around him.

Earlier, he woke up to the sounds of explosions and gunfire, the former shaking the building he currently in, and the later following shortly, screams echoing through the complex signifying the results.

Like any normal person, he tried to run away to safety, away from the apparent battlefield. He exited the apartment he woke up in, running through corridors looking for exits.

In the back of his mind he wondered where the hell was he, anyway?

His musings were cut short as another explosion shook the building, several segments of the floor he was on falling off below.

Not wishing to fall to his death, he ran to the somewhere more stable, stumbling to the hall just in time to see the tall and bulky automated heavy combat droid mowing down military men, at least he assumed they were.

One surviving soldier tried to retreat, running to were he was currently, but was gunned down to pieces right in front of him.

The droid at that point acquired a new target: Him.

Too shocked from seeing somebody being killed to move, he saw the droid launching the rocket at his position.

His entire life flashed before his eyes, which only consisted from waking up in that apartment and running here to take a rocket to the face. At that very brief moment he realized that he didn't know who he was.

He was tackled to the ground, and the rocket passed above him and exploding somewhere far behind him.

Unfortunately for him and his savior, the rocket hit the support pillar for this floor, weakening the integrity. And if that wasn't enough, another bigger explosion shook the building, collapsing the floor they were on.

Before going unconscious from hitting his head on something hard, he noted that his savior has blue hair.

When he came to, his vision was blurry, but he could see that the power gave out, leaving him in the darkness, illuminated by fire that spread as the result of the battle. Speaking of the battle, he didn't hear gunshots anymore.

He tried to move, but he was too weak from the fall or worse, broken his spine.

Trying to check his surroundings (his senses still worked thankfully), he felt that he was holding something, or rather, somebody.

The person that saved him earlier was a girl, with short blue hair and pale skin, alive but unconscious according to her breathing and the trail of blood coming from her head.

With some of his senses gaining back some of their functions, he noted that they were dragged across the floor by someone.

When his vision stopped being blurry, he saw a girl holding him, trying to get them away from the dangerously unstable areas and the fire, her hair was long and red, and if the bandages were any indication, she was injured.

She was getting weaker and weaker, so she dragged them to the place that was not claimed by the fire yet, and put them into the best comfortable position their injuries allowed, and then she fallen unconscious, lying besides them.

He envied the unconscious girls, as for some reason he had enough strength to stay conscious, only to see the fires slowly creep closer and closer to them.

After what seemed to be hours, he was apathetic enough to the fact that he would die soon that he wished the fire to move faster. At least the girls will die peacefully.

Just as he was finally, to his relief, starting to lose consciousness, he heard someone shouting about survivors.

* * *

He woke up to the unfamiliar ceiling, which also doubled as a mirror, and so he also woke up to the sight of slightly-androgynous fourteen years old boy with brownish-black hair and green eyes (or were they blue?).

Now that he though about it, the ceiling at that apartment was unfamiliar too, but he was too much in the hurry to think about it.

He tried to stand up from the bed, but the pain from his back prevented it.

"Sir, while the damage to the spine was lighter than we expected, it is advised that you refrain from sudden motions" came the robotic voice from the speaker above him.

Carefully sitting on the bed, he looked around him. He was in the hospital, lying on the bed in the room filled patients with various states of injury.

But what captured his attention were two girls about his age. The girls who saved him. And they were looking at him.

One was a pale girl with blue hair and red eyes, staring blankly at him.

The other was the redhead with long hair and blue eyes, who looked at him with the mix of confusion and irritation.

Their bandages mirrored each other.

The doors opened and the doctors and some official looking men entered.

The doctors checked the injuries while the suits asked questions about some attack on the Neo-Hakone residential complex. He guessed that is where he was earlier.

When it was his turn, he recounted the events as he remembered him. And then they asked about him.

"I'm Shinji Ikari, and I… I…" Was all he said before what he tried not to think about finally hit him.

Besides the name, there was absolutely nothing in his mind. Little did he know that the girls had gone through this too.

If this at least two weeks ago, their names would have not matched anything in the databases and the suits would have snatched them right there for suspected attempt of espionage by pretending to be amnesiacs (especially with those psi-operatives that masked their mind), since everybody, that is everybody legal, were on the database, their whole history and everything else. Not being in the databases meant that you were the ghost that tried to hide him/herself from the prying eyes of the security agencies.

But that was two weeks ago, because one week ago there was the large hacker invasion on the UNN (United Nations Nominate) Administration servers responsible for Eastern Asia, resulting in massive information loss, including the citizen profiles. Not even the backups were spared.

Almost immediately, the group of the most powerful Japanese Zaibatsu tried to stage a Coup d'etat on the UNN. But now the UNN military is winning with overwhelming results, and the rumors that the Zaibatsu heads committed suicides were now circulating the net.

As a result, the agencies were too busy with the aftermath to bother with what could be simply a genuine case of amnesia.

How convenient.

As he was left shaken, he didn't notice a presence at the side of his bed.

"Are you alright?" asked a voice.

He looked up to see the girls with worried looks on their faces.

"I'm fine" He lied

They obviously didn't buy that.

"Everything's going to be alright." The blue haired one spoke softly.

"It will be waste otherwise, after all the trouble you put me through." The redhead said.

For some reason he felt better after those words.

"Thank you miss…" He begun to say.

"Rei Ayanami" Said the blue haired girl.

"And I'm Asuka Langley Soryu" Said the redhead.

It was year 2106. And it was the first day of their lives.

* * *

After some paperwork, they were placed into the orphanage.

To say that the following four years until their adulthood were interesting was an understatement.

Their relationship with each other constantly shifted between from friends to enemies to indifference to almost lover-like interaction to being just friends again and so on.

All other children told them to make up their minds.

When they turned 18 (they had a same birthday they decided on, since they didn't know their original ones), they were friends that just wanted to be away from each other, if that makes sense.

Which explained the slightly tense situation in the traincab where all three were currently sitting in.

It was a half a year since they gone into the world to live by themselves, and by the looks of things none of them could get a job in civilian and private sectors, and the nanites that the orphanage gave them were not going to support them forever. For all the measures that the UNN applies to prevent corporate rule and to make sure that something like SHODAN never happens again, it really hurt the economy with their bureaucracy, especially for lower-middle and lower classes.

The only option now was to join the military.

They didn't talked during the ride, they didn't talked when they entered the Ramsey Recruitment Center, they didn't talked when they were using the simulations which explained the basics of military work, and now they stood between three passageways that led to the shuttles: One to join the Marines, One to join the Navy and One to join the O.S.A., the rumored PSI black ops. And they didn't spoke a word.

"Rei, Asuka…" Shinji broke the silence, not looking at the girls.

"What?" Asuka asked. Rei remained silent.

"…Good luck." He said.

Despite herself, Asuka smiled.

"You too, idiot." She said.

"Be careful, both of you." Rei finally said.

Slightly surprised but used to the blue-haired girl's personality, both Shinji and Asuka recovered.

"You too, Rei" He replied

"Don't go easy on me, Wondergirl." Asuka replied, with no hostility usually associated with that nickname.

And so they parted ways.

Rei walked away to the O.S.A.

Asuka marched to the Marines.

And Shinji joined the Navy.

It was year 2110, and the public was going crazy over the possibilities of FTL travel.

* * *

On the first moon of Jupiter, Io, the Navy maintained the survival training school.

Pros: It gave those who completed the training course the endurance and stamina that few could compete with, and the survival skills that made soldiers deadly.

Cos: 21.2% fatality rate, the bickering between the Marines and the Navy personnel, and the possibility of being secretly used by OSA deep cover operatives to improve their own build.

And the most recent Con: The top brass demands that the interservice cooperation must be improved.

Most of cadets are wandering if there is such thing as "interservice cooperation".

For that cooperation, the instructions formed the teams of three, one member from each branch of the military.

As if the universe was doing a favor (or making a joke at their own expense, it was hard to tell), one such team consisted of Shinji Ikari, Rei Ayanami and Asuka Langley Soryu.

While they were somewhat happy to see each other, bickering friends didn't make for good teamwork.

In these two years, Asuka Langely Soryu made herself quite the reputation among the marines.

Coming with one of the highest scores the boot camp instructors ever saw, she was recommended to attend the Polidies Training Center. In addition to being a training school, it had a thriving black market for weapons, where she got some neat goodies. To her irritation, some idiot overthrown the official powers that be and proclaimed himself Magnate of Polidies. To her joy, he gave a nice opportunity to test out those black market goodies, with him and his men as targets. As a bonus, acting on the orders of peacekeeping marines that shortly arrived, she ransacked the black market for more goodies, making herself quite knowledgeable on weapons.

Impressed, the command proposed to her to join the marine assault on the mining facilities on the JM-432 asteroid picket, which was fully automated (crewed by robots), and so was a very valuable target for hackers, since the mines were the main source of materials that goes to the shipyards, and the Navy would whine if their precious ships broke down.

And lo and behold, some Hacker was successful in taking over the mines.

The facilities were eventually be recaptured, but the surviving marines will call this operation the "The Second Citadel Station" what with the robots at every step, behind every corner, with those tiny claustrophobic tunnels with no light sources. They managed to cut the hacker's connection to the CPU that controlled the robots, and while the nightmares of tiny tunnels would haunt her for some time, Asuka soon proved herself to be a Heavy weapons expert and knew the robot's weaknesses as far as standard designs are concerned.

For her third year in service, she applied for Io Survival Training School, where she met her friends that weren't macho marines.

Rei Ayanami was a OSA brass dream come true.

As soon as Rei stepped on OSA basic training facility, the less skilled instructors told her to stop dyeing her hair (to which she replied that it was natural), while the skilled instructors already saw her seemly impossibly organized mind, sensed the potential for growth.

Soon she applied for transfer to TOS Ru Nang, where she among other potential operatives where placed in Sensory Deprivation Tanks for the most of the year, opening their PSI potential. During this Year, her will has grown. She was now capable of freezing her enemies and manipulate distant objects, and now the foundation for what the officials called the "second tier disciplines" were opened for her. Far sooner than any of her tankmates by a large margin.

The Overseers were puzzled however, of why she dreamed of multiple selves submerged in some orange liquid.

More than satisfied with her growth, the Command decided to train her in Field Operations, and Rei chose the Selections Group. There they trained her as an assassin, nourishing her to be the very motion of death, the grim reaper who removes the dangerous pieces from the board, in order to ensure that the flow is not disturbed in the game called life. That way she learned to PSI-enhance her reflexes to use the weapons with deadly skills.

In very rare moments, the instructors who monitored her mind saw a briefest of glimpses of a bearded man with orange shades, with interlaced hands hiding his face.

For her third year, on the advice that the neglected body should be trained, she applied for the Io Survival Training School, now without going into Deep Cover as standard procedure for OSA, as the Top Brass requested for "Interservice Cooperation". There she met the only people she called friends.

Shinji Ikari was not in any way famous, and it suited him just fine.

Fresh out of the Navy boot camp, he applied for transfer to UNN Lucille as a ship operator, learning navigational systems and the technology behind it. Captain Mayer was pleased with his work. As an added bonus, a friendly ensign showed him a backdoor in the ship's dataloop, which allowed him to access some "interesting" information (he was only 19 after all). All this resulted in him becoming quite proficient with any kind of software (the "interesting" information wasn't the only thing on the net after all)

The next year wasn't so carefree.

He applied for the newly build Heavy Cruiser Carfax. The mission of Carfax's crew was to research the new type of comet that will be passing by near the outer regions of the solar system.

They did the job, and the eggheads back home will be happy with the data. Unfortunately for Shinji and the rest of the crew, the small piece of comet separated from the main mass and struck the Carfax. There were 123 casualties, including the chief navigation officer. With Shinji filling the shoes, the damaged Heavy Cruiser Carfax limped home, suffering system breakdowns along the way. With guiding the ship and repairing the systems, Shinji acquired more knowledge about cybernetics than he cared to, with someone calling it Cyber-Affinity.

And so, for his third year in service, he applied for Io Survival Training School in order to be prepared for another such incident, where he met the girls of his dreams (not that he will admit it).

And so, for the half of year, the three branches of the military strengthen their bonds.

That is to say, increased their mutual hatred of each other.

The traditional rivalry between the Marines and the Navy reared its head, and the OSA ops spooked everybody.

As for our "children", they had their own problems:

Asuka preferred to act solo.

Rei was trained to act solo.

And Shinji was simply not prepared for this stuff.

Just as the Brass was about to call it quits and proclaim the "cooperation" a failure, disaster struck. The Hostile to UNN elements decided to cripple the military by taking out one of the most prestigious training centers, Io Survival Training School.

The hackers took over the security systems, turning them against their former masters, killing everybody that got in their sensors. In only few hours, the fatality rate of Io jumped to 57%, this including the school staff.

If that wasn't enough, the hackers opened the cages that housed the Gorilla/Tiger hybrid mutants that were created by SHODAN in the Citadel Station 41 years ago. The ancestors of these mutants were captured during the boarding of the jettisoned bridge, after the Hacker destroyed SHODAN. In addition of researching them in order to find out what SHODAN used to create her viruses, the military bred them for training purposes, like making the soldiers fight these on Io. Most of the 21.2% fatality rate came from these, making the soldiers wonder how the hell the combat untrained hacker was able to survive in Citadel.

The trainees had enough problems dealing with few of them, but when all of them are released at the same time, they almost had no chance.

Almost

As if the extreme situation was the trigger, the "children" started acting.

Asuka, with her assault rifle and lots of explosives, blown the robots to pieces before they could lock on her, outdanced the mutants and filled them with holes, nothing passed her, nothing outran her, nothing escaped her wrath.

Rei, with her Psi-amplifier, froze the opposition, "force used" nearby things to her advantage, silently ambushed the enemy, backstabbing the hostile security, all with the deadly machine-like precision that scared everybody but her friends.

Both were covering Shinji, who used his skills to disable the hostile security, was getting them access to areas that the system refused them entry, jury-rig security robots to fight for them, and finally reprogram the security back to their side and to cut the hacker's access to the complex.

They survived…Barely.

When they realized it, they started to laugh, even Rei, who let out quiet chuckles.

At the end of this all, Io Survival Training School was recaptured, with the fatality rate of 89.6%.

It was year 2113, and all of this was overshadowed by the news that the first FTL-capable ship Von Braun was nearing its completion, and thus the realization of the dream of human expansion into space.

* * *

Captain William Bedford Diego (actual rank Rear Admiral) was going over the personnel recruitment.

Despite his influence and Delacroix's warnings about the potential dangers of FTL-engines, the committee approved of the idiotic premature launching of the ship. He was certain that he have Korenchkin to "thank" for that, the ruthless but competent official of TriOptimum corporation.

At least he was able to convince the committee to make the UNN ship escort Von Braun (Delacroix was already figuring out how to enable the non-FTL ship to follow the FTL-able ship) so that he could keep an eye on Korenchkin.

And for that goal, he was recruiting capable people to serve him and the UNN on the Rickenbacker, the heavy destroyer that will be escorting Von Braun.

And in doing so, he came across the files of Shinji Ikari, Rei Ayanami and Asuka Langley Soryu.

Three completely different people, with only the amnesia and four years living at the orphanage connecting them.

Three young people struggling against everything the world had thrown at them.

In the way, they reminded him of his younger self, when after the events of Citadel station he and his family effectively became an outcasts for being related to Edward Diego, who is now regarded as man who nearly destroyed humanity because of his greed, because he was responsible for the monster called SHODAN. His mother couldn't take the pressure, and she ended her life in the bathtub with sliced arteries, and he, William Diego, found her like that. It was after Mother's death that he truly started to hate his father, and subsequently everything corporate (except for his wife, who was one of the few rational and humane corporate directors he met), joining the UNN military, rising through the ranks despite the stigma of being the son of Edward Diego, and soon that vice was replaced with the virtue of being the Hero of Boston Harbor, the rational face of UNN.

Shaking himself out of his memories, he decides to approve their applications, for while they technically were still rookies, they proved themselves last year at Io and unlike old veterans, rookies were known to be inventive.

Now to make sure that the Von Braun will actually be a ship on its maiden voyage instead of rushed stitched-together junk-heap with the FTL-drive attached to it.

* * *

Order: Reassign *****/*

From: Captain William Bedford Diego, UNN Rickenbacker

To: Soldier ******-*

Re: Assignment to Von Braun escort mission.

Solider-

Your application to join the crew of the Rickenbacker has been approved.

Report to shuttle Mayfair at port Francisco at 0400 on 01-09-14.

Get ready to become part of history, soldier.

WBD.

* * *

Author's note:

Was having a nostalgia, got myself replaying System Shock 2 and finally got the original System Shock to work with good quality and that sexy SHODAN voice.

Also, as good SS2 is (Bioshock is mere shadow of it despite it being one of the best games I've played) it had some serious balancing issues, especially with guns, where Standard weapons, thanks to their low minimum stat recruitments, were more powerful thanks to having more bonuses than the high minimum stat recruitments heavy, energy and exotic weapons (except the Crystal shard). So those who played SS2, please pretend that this version of the game is using some balance patch/mod that makes the heavy, energy and exotic weapons not useless by the end-game, plus some balancing of tech skills and PSI disciplines.

That said, I don't know If I will be able to continue this (exams, the bane of all fanfic writers).


End file.
